Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1727 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0726964336 sf0726963342 7 26964336 3.61E-07 3.61E-07
vg0819603039 sf0819600326 8 19603039 5.49E-07 5.49E-07
vg0115927407 sf0115926381 1 15927407 1.45E-06 1.45E-06
vg0119699388 sf0119698343 1 19699388 1.81E-06 1.81E-06
vg1104990849 sf1104986660 11 4990849 2.42E-06 2.42E-06
vg0119838948 sf0119837903 1 19838948 2.93E-06 2.93E-06
vg0523235966 sf0523173387 5 23235966 5.17E-06 5.17E-06